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Terreros MC, Rowold D, Luis JR, Khan F, Agrawal S, Herrera RJ. North Indian Muslims: enclaves of foreign DNA or Hindu converts? AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 133:1004-12. [PMID: 17427927 DOI: 10.1002/ajpa.20600] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The mtDNA composition of two Muslim sects from the northern Indian province of Uttar Pradesh, the Sunni and Shia, have been delineated using sequence information from hypervariable regions 1 and 2 (HVI and HVII, respectively) as well as coding region polymorphisms. A comparison of this data to that from Middle Eastern, Central Asian, North East African, and other Indian groups reveals that, at the mtDNA haplogroup level, both of these Indo-Sunni and Indo-Shia populations are more similar to each other and other Indian groups than to those from the other regions. In addition, these two Muslim sects exhibit a conspicuous absence of West Asian mtDNA haplogroups suggesting that their maternal lineages are of Indian origin. Furthermore, it is noteworthy that the maternal lineage data indicates differences between the Sunni and Shia collections of Uttar Pradesh with respect to the relative distributions of Indian-specific M sub-haplogroups (Indo Shia > Indo Sunni) and the R haplogroup (Indo Sunni > Indo Shia), a disparity that does not appear to be related to social status or geographic regions within India. Finally, the mtDNA data integrated with the Y-chromosome results from an earlier study, which indicated a major Indian genetic (Y-chromosomal) contribution as well, suggests a scenario of Hindu to Islamic conversion in these two populations. However, given the substantial level of the African/Middle Eastern YAP lineage in the Indo-Shia versus its absence in the Indo-Sunni, it is likely that this conversion was somewhat gender biased in favor of females in the Indo-Shia.
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Affiliation(s)
- Maria C Terreros
- Department of Biological Sciences, Florida International University, University Park, Miami, FL 33199, USA
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152
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Petraglia M, Korisettar R, Boivin N, Clarkson C, Ditchfield P, Jones S, Koshy J, Lahr MM, Oppenheimer C, Pyle D, Roberts R, Schwenninger JL, Arnold L, White K. Middle Paleolithic assemblages from the Indian subcontinent before and after the Toba super-eruption. Science 2007; 317:114-6. [PMID: 17615356 DOI: 10.1126/science.1141564] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The Youngest Toba Tuff (YTT) eruption, which occurred in Indonesia 74,000 years ago, is one of Earth's largest known volcanic events. The effect of the YTT eruption on existing populations of humans, and accordingly on the course of human evolution, is debated. Here we associate the YTT with archaeological assemblages at Jwalapuram, in the Jurreru River valley of southern India. Broad continuity of Middle Paleolithic technology across the YTT event suggests that hominins persisted regionally across this major eruptive event.
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Affiliation(s)
- Michael Petraglia
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, UK.
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153
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González AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM. Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics 2007; 8:223. [PMID: 17620140 PMCID: PMC1945034 DOI: 10.1186/1471-2164-8-223] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Accepted: 07/09/2007] [Indexed: 11/19/2022] Open
Abstract
Background The out of Africa hypothesis has gained generalized consensus. However, many specific questions remain unsettled. To know whether the two M and N macrohaplogroups that colonized Eurasia were already present in Africa before the exit is puzzling. It has been proposed that the east African clade M1 supports a single origin of haplogroup M in Africa. To test the validity of that hypothesis, the phylogeographic analysis of 13 complete mitochondrial DNA (mtDNA) sequences and 261 partial sequences belonging to haplogroup M1 was carried out. Results The coalescence age of the African haplogroup M1 is younger than those for other M Asiatic clades. In contradiction to the hypothesis of an eastern Africa origin for modern human expansions out of Africa, the most ancestral M1 lineages have been found in Northwest Africa and in the Near East, instead of in East Africa. The M1 geographic distribution and the relative ages of its different subclades clearly correlate with those of haplogroup U6, for which an Eurasian ancestor has been demonstrated. Conclusion This study provides evidence that M1, or its ancestor, had an Asiatic origin. The earliest M1 expansion into Africa occurred in northwestern instead of eastern areas; this early spread reached the Iberian Peninsula even affecting the Basques. The majority of the M1a lineages found outside and inside Africa had a more recent eastern Africa origin. Both western and eastern M1 lineages participated in the Neolithic colonization of the Sahara. The striking parallelism between subclade ages and geographic distribution of M1 and its North African U6 counterpart strongly reinforces this scenario. Finally, a relevant fraction of M1a lineages present today in the European Continent and nearby islands possibly had a Jewish instead of the commonly proposed Arab/Berber maternal ascendance.
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Affiliation(s)
- Ana M González
- Department of Genetics, Faculty of Biology, University of La Laguna, Tenerife 38271, Spain
| | - José M Larruga
- Department of Genetics, Faculty of Biology, University of La Laguna, Tenerife 38271, Spain
| | - Khaled K Abu-Amero
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh 11211, Saudi Arabia
| | - Yufei Shi
- Department of Genetics, King Faisal Specialist Hospital & Research Center, Riyadh 11211, Saudi Arabia
| | - José Pestano
- Department of Genetics, Faculty of Medicine, University of Las Palmas de Gran Canaria, Las Palmas 35080, Spain
| | - Vicente M Cabrera
- Department of Genetics, Faculty of Biology, University of La Laguna, Tenerife 38271, Spain
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154
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Zhang F, Su B, Zhang YP, Jin L. Genetic studies of human diversity in East Asia. Philos Trans R Soc Lond B Biol Sci 2007; 362:987-95. [PMID: 17317646 PMCID: PMC2435565 DOI: 10.1098/rstb.2007.2028] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
East Asia is one of the most important regions for studying evolution and genetic diversity of human populations. Recognizing the relevance of characterizing the genetic diversity and structure of East Asian populations for understanding their genetic history and designing and interpreting genetic studies of human diseases, in recent years researchers in China have made substantial efforts to collect samples and generate data especially for markers on Y chromosomes and mtDNA. The hallmark of these efforts is the discovery and confirmation of consistent distinction between northern and southern East Asian populations at genetic markers across the genome. With the confirmation of an African origin for East Asian populations and the observation of a dominating impact of the gene flow entering East Asia from the south in early human settlement, interpretation of the north-south division in this context poses the challenge to the field. Other areas of interest that have been studied include the gene flow between East Asia and its neighbouring regions (i.e. Central Asia, the Sub-continent, America and the Pacific Islands), the origin of Sino-Tibetan populations and expansion of the Chinese.
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Affiliation(s)
- Feng Zhang
- Institute of Genetics, School of Life Sciences, Fudan UniversityShanghai 200433, People's Republic of China
| | - Bing Su
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, People's Republic of China
| | - Ya-ping Zhang
- Laboratory of Cellular and Molecular Evolution, Kunming Institute of Zoology, Chinese Academy of SciencesKunming 650223, People's Republic of China
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan UniversityKunming 650091, People's Republic of China
| | - Li Jin
- Institute of Genetics, School of Life Sciences, Fudan UniversityShanghai 200433, People's Republic of China
- CAS-MPG Partner Institute of Computational Biology, Chinese Academy of SciencesShanghai 200031, People's Republic of China
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155
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Hudjashov G, Kivisild T, Underhill PA, Endicott P, Sanchez JJ, Lin AA, Shen P, Oefner P, Renfrew C, Villems R, Forster P. Revealing the prehistoric settlement of Australia by Y chromosome and mtDNA analysis. Proc Natl Acad Sci U S A 2007; 104:8726-30. [PMID: 17496137 PMCID: PMC1885570 DOI: 10.1073/pnas.0702928104] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Published and new samples of Aboriginal Australians and Melanesians were analyzed for mtDNA (n=172) and Y variation (n=522), and the resulting profiles were compared with the branches known so far within the global mtDNA and the Y chromosome tree. (i) All Australian lineages are confirmed to fall within the mitochondrial founder branches M and N and the Y chromosomal founders C and F, which are associated with the exodus of modern humans from Africa approximately 50-70,000 years ago. The analysis reveals no evidence for any archaic maternal or paternal lineages in Australians, despite some suggestively robust features in the Australian fossil record, thus weakening the argument for continuity with any earlier Homo erectus populations in Southeast Asia. (ii) The tree of complete mtDNA sequences shows that Aboriginal Australians are most closely related to the autochthonous populations of New Guinea/Melanesia, indicating that prehistoric Australia and New Guinea were occupied initially by one and the same Palaeolithic colonization event approximately 50,000 years ago, in agreement with current archaeological evidence. (iii) The deep mtDNA and Y chromosomal branching patterns between Australia and most other populations around the Indian Ocean point to a considerable isolation after the initial arrival. (iv) We detect only minor secondary gene flow into Australia, and this could have taken place before the land bridge between Australia and New Guinea was submerged approximately 8,000 years ago, thus calling into question that certain significant developments in later Australian prehistory (the emergence of a backed-blade lithic industry, and the linguistic dichotomy) were externally motivated.
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Affiliation(s)
- Georgi Hudjashov
- Estonian Biocentre and Tartu University, Department of Evolutionary Biology, Riia 23, 51010 Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre and Tartu University, Department of Evolutionary Biology, Riia 23, 51010 Tartu, Estonia
- Leverhulme Centre for Human Evolutionary Studies, University of Cambridge, Cambridge CB2 1QH, United Kingdom
- To whom correspondence may be addressed. E-mail: or
| | - Peter A. Underhill
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120
| | - Phillip Endicott
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
| | - Juan J. Sanchez
- National Institute of Toxicology and Forensic Science, Canary Islands Delegation, Campus de Ciencias de la Salud, 38320 La Laguna, Tenerife, Spain
| | - Alice A. Lin
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305-5120
| | - Peidong Shen
- Stanford Genome Technology Center, Palo Alto, CA 94304
| | - Peter Oefner
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Strasse 9, 93053 Regensburg, Germany
| | - Colin Renfrew
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, United Kingdom; and
- To whom correspondence may be addressed. E-mail: or
| | - Richard Villems
- Estonian Biocentre and Tartu University, Department of Evolutionary Biology, Riia 23, 51010 Tartu, Estonia
| | - Peter Forster
- Department of Forensic Science and Chemistry, Faculty of Science and Technology, Anglia Ruskin University, East Road, Cambridge CB1 1PT, United Kingdom
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156
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Gayden T, Cadenas AM, Regueiro M, Singh NB, Zhivotovsky LA, Underhill PA, Cavalli-Sforza LL, Herrera RJ. The Himalayas as a directional barrier to gene flow. Am J Hum Genet 2007; 80:884-94. [PMID: 17436243 PMCID: PMC1852741 DOI: 10.1086/516757] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2007] [Accepted: 02/23/2007] [Indexed: 11/03/2022] Open
Abstract
High-resolution Y-chromosome haplogroup analyses coupled with Y-short tandem repeat (STR) haplotypes were used to (1) investigate the genetic affinities of three populations from Nepal--including Newar, Tamang, and people from cosmopolitan Kathmandu (referred to as "Kathmandu" subsequently)--as well as a collection from Tibet and (2) evaluate whether the Himalayan mountain range represents a geographic barrier for gene flow between the Tibetan plateau and the South Asian subcontinent. The results suggest that the Tibetans and Nepalese are in part descendants of Tibeto-Burman-speaking groups originating from Northeast Asia. All four populations are represented predominantly by haplogroup O3a5-M134-derived chromosomes, whose Y-STR-based age (+/-SE) was estimated at 8.1+/-2.9 thousand years ago (KYA), more recent than its Southeast Asian counterpart. The most pronounced difference between the two regions is reflected in the opposing high-frequency distributions of haplogroups D in Tibet and R in Nepal. With the exception of Tamang, both Newar and Kathmandu exhibit considerable similarities to the Indian Y-haplogroup distribution, particularly in their haplogroup R and H composition. These results indicate gene flow from the Indian subcontinent and, in the case of haplogroup R, from Eurasia as well, a conclusion that is also supported by the admixture analysis. In contrast, whereas haplogroup D is completely absent in Nepal, it accounts for 50.6% of the Tibetan Y-chromosome gene pool. Coalescent analyses suggest that the expansion of haplogroup D derivatives--namely, D1-M15 and D3-P47 in Tibet--involved two different demographic events (5.1+/-1.8 and 11.3+/-3.7 KYA, respectively) that are more recent than those of D2-M55 representatives common in Japan. Low frequencies, relative to Nepal, of haplogroup J and R lineages in Tibet are also consistent with restricted gene flow from the subcontinent. Yet the presence of haplogroup O3a5-M134 representatives in Nepal indicates that the Himalayas have been permeable to dispersals from the east. These genetic patterns suggest that this cordillera has been a biased bidirectional barrier.
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Affiliation(s)
- Tenzin Gayden
- Department of Biological Sciences, Florida International University, Miami, FL 33199, USA
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157
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Abstract
A survey of the genetic ancestry of 125 Cambodian children resident in Siem Reap province was undertaken, based on eight Y-chromosome binary polymorphisms and sequencing of the mtDNA HV1 region. The data indicated a largely East Asian paternal ancestry and a local Southeast Asian maternal ancestry. The presence of Y-chromosomes P* and R1al* was suggestive of a small but significant Indo-European male ancestral component, which probably reflects the history of Indian, and later European, influences on Cambodia.
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Affiliation(s)
- M L Black
- Centre for Human Genetics, Edith Cowan University, Perth, Australia
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158
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Genetic affinities between endogamous and inbreeding populations of Uttar Pradesh. BMC Genet 2007; 8:12. [PMID: 17417972 PMCID: PMC1855350 DOI: 10.1186/1471-2156-8-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Accepted: 04/07/2007] [Indexed: 11/12/2022] Open
Abstract
Background India has experienced several waves of migration since the Middle Paleolithic. It is believed that the initial demic movement into India was from Africa along the southern coastal route, approximately 60,000–85,000 years before present (ybp). It has also been reported that there were two other major colonization which included eastward diffusion of Neolithic farmers (Elamo Dravidians) from Middle East sometime between 10,000 and 7,000 ybp and a southern dispersal of Indo Europeans from Central Asia 3,000 ybp. Mongol entry during the thirteenth century A.D. as well as some possible minor incursions from South China 50,000 to 60,000 ybp may have also contributed to cultural, linguistic and genetic diversity in India. Therefore, the genetic affinity and relationship of Indians with other world populations and also within India are often contested. In the present study, we have attempted to offer a fresh and immaculate interpretation on the genetic relationships of different North Indian populations with other Indian and world populations. Results We have first genotyped 20 tetra-nucleotide STR markers among 1800 north Indian samples of nine endogamous populations belonging to three different socio-cultural strata. Genetic distances (Nei's DA and Reynold's Fst) were calculated among the nine studied populations, Caucasians and East Asians. This analysis was based upon the allelic profile of 20 STR markers to assess the genetic similarity and differences of the north Indian populations. North Indians showed a stronger genetic relationship with the Europeans (DA 0.0341 and Fst 0.0119) as compared to the Asians (DA 0.1694 and Fst – 0.0718). The upper caste Brahmins and Muslims were closest to Caucasians while middle caste populations were closer to Asians. Finally, three phylogenetic assessments based on two different NJ and ML phylogenetic methods and PC plot analysis were carried out using the same panel of 20 STR markers and 20 geo-ethnic populations. The three phylogenetic assessments revealed that north Indians are clustering with Caucasians. Conclusion The genetic affinities of Indians and that of different caste groups towards Caucasians or East Asians is distributed in a cline where geographically north Indians and both upper caste and Muslim populations are genetically closer to the Caucasians.
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159
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Y-chromosome evidence suggests a common paternal heritage of Austro-Asiatic populations. BMC Evol Biol 2007; 7:47. [PMID: 17389048 PMCID: PMC1851701 DOI: 10.1186/1471-2148-7-47] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 03/28/2007] [Indexed: 11/12/2022] Open
Abstract
Background The Austro-Asiatic linguistic family, which is considered to be the oldest of all the families in India, has a substantial presence in Southeast Asia. However, the possibility of any genetic link among the linguistic sub-families of the Indian Austro-Asiatics on the one hand and between the Indian and the Southeast Asian Austro-Asiatics on the other has not been explored till now. Therefore, to trace the origin and historic expansion of Austro-Asiatic groups of India, we analysed Y-chromosome SNP and STR data of the 1222 individuals from 25 Indian populations, covering all the three branches of Austro-Asiatic tribes, viz. Mundari, Khasi-Khmuic and Mon-Khmer, along with the previously published data on 214 relevant populations from Asia and Oceania. Results Our results suggest a strong paternal genetic link, not only among the subgroups of Indian Austro-Asiatic populations but also with those of Southeast Asia. However, maternal link based on mtDNA is not evident. The results also indicate that the haplogroup O-M95 had originated in the Indian Austro-Asiatic populations ~65,000 yrs BP (95% C.I. 25,442 – 132,230) and their ancestors carried it further to Southeast Asia via the Northeast Indian corridor. Subsequently, in the process of expansion, the Mon-Khmer populations from Southeast Asia seem to have migrated and colonized Andaman and Nicobar Islands at a much later point of time. Conclusion Our findings are consistent with the linguistic evidence, which suggests that the linguistic ancestors of the Austro-Asiatic populations have originated in India and then migrated to Southeast Asia.
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160
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Luca F, Di Giacomo F, Benincasa T, Popa LO, Banyko J, Kracmarova A, Malaspina P, Novelletto A, Brdicka R. Y-chromosomal variation in the Czech Republic. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2007; 132:132-9. [PMID: 17078035 DOI: 10.1002/ajpa.20500] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
To analyze the contribution of the Czech population to the Y-chromosome diversity landscape of Europe and to reconstruct past demographic events, we typed 257 males from five locations for 21 UEPs. Moreover, 141 carriers of the three most common haplogroups were typed for 10 microsatellites and coalescent analyses applied. Sixteen Hg's characterized by derived alleles were identified, the most common being R1a-SRY(10831) and P-DYS257*(xR1a). The pool of haplogroups within I-M170 represented the third most common clade. Overall, the degree of population structure was low. The ages for Hg I-M170, P-DYS257*(xR1a), and R1a-SRY(10831) ap peared to be comparable and compatible with their presence during or soon after the LGM. A signal of population growth beginning in the first millennium B.C. was detected. Its similarity among the three most common Hg's indicated that growth was characteristic for a gene pool that already contained all of them. The Czech population appears to be influenced, to a very moderate extent, by genetic inputs from outside Europe in the post-Neolithic and historical times. Population growth postdated the archaeologically documented introduction of Neolithic technology and the estimated central value coincides with a period of repeated changes driven by the development of metal technologies and the associated social and trade organization.
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Affiliation(s)
- F Luca
- Department of Cell Biology, University of Calabria, Rende, Italy
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161
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Chaubey G, Metspalu M, Kivisild T, Villems R. Peopling of South Asia: investigating the caste-tribe continuum in India. Bioessays 2007; 29:91-100. [PMID: 17187379 DOI: 10.1002/bies.20525] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In recent years, mtDNA and Y chromosome studies involving human populations from South Asia and the rest of the world have revealed new insights about the peopling of the world by anatomically modern humans during the late Pleistocene, some 40,000-60,000 years ago, over the southern coastal route from Africa. Molecular studies and archaeological record are both largely consistent with autochthonous differentiation of the genetic structure of the caste and tribal populations in South Asia. High level of endogamy created by numerous social boundaries within and between castes and tribes, along with the influence of several evolutionary forces such as genetic drift, fragmentation and long-term isolation, has kept the Indian populations diverse and distant from each other as well as from other continental populations. This review attempts to summarize recent genetic studies on Indian caste and tribal populations with the focus on the information embedded in the socially defined structure of Indian populations.
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Affiliation(s)
- Gyaneshwer Chaubey
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia.
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162
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Gibert M, Touinssi M, Reviron D, Mercier P, Boëtsch G, Chiaroni J. HLA-DRB1 frequencies of the Comorian population and their genetic affinities with Sub-Saharan African and Indian Oceanian populations. Ann Hum Biol 2007; 33:265-78. [PMID: 17092866 DOI: 10.1080/03014460600578599] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND Ethnic-historic sources have considered the Comorian population to be the result of an amalgamation of African, Arabian and Southeast Asian groups. AIM This study seeks to determine the genetic relationships and contributions from Sub-Saharan Africa and Indian Oceania and to reconstruct past migration events. SUBJECTS AND METHODS The human leukocyte antigen (HLA) polymorphism of a Comorian population was described and analysed. RESULTS Genetic distances and multidimensional scaling analyses showed complex patterns of genetic differentiation in the Indian Oceanian area as a result of continuous gene flow occurring within the past approximately 2500 years. Nevertheless, the Comorian genetic pool appears to be a mix of Bantu-speaking and Arab populations as testified to by admixture estimations of almost 50-60% and 27-33%, respectively. CONCLUSION The Comorian population may represent the eastern limit of the recent and massive eastward Bantu expansion. In contrast to the population from Madagascar (Merina), only a restricted influence of Austronesian populations was found.
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Affiliation(s)
- M Gibert
- Centre d'Anthropologie, UMR 8555, CNRS, Toulouse, France.
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163
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Kennerknecht I, Plümpe N, Edwards S, Raman R. Hereditary prosopagnosia (HPA): the first report outside the Caucasian population. J Hum Genet 2006; 52:230-236. [PMID: 17186317 DOI: 10.1007/s10038-006-0101-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Accepted: 12/06/2006] [Indexed: 10/23/2022]
Abstract
Prosopagnosia (PA) or face blindness is characterized by a deficiency in identifying familiar faces. Almost all reports are single cases or collections of unrelated patients who acquired prosopagnosia after brain injuries, strokes or atrophy of at least the right occipito-temporal cortex. Until 2001, the inborn form - in the absence of any brain lesions - was described in fewer than 20 probands exclusively of Caucasian origin. We recently found that in the German Caucasian population, congenital prosopagnosia has a very high prevalence of at least 2.5% and that it is genetically determined. It is best described by autosomal-dominant inheritance in the more than 50 families investigated. We therefore introduced the term non-syndromic hereditary PA for the congenital form of a monosymptomatic or isolated PA. This surprisingly high frequency in the Caucasian population prompted us to extend our search to other ethnic groups. We performed a questionnaire-based screening among 198 native Indian students at Banaras Hindu University in Varanasi. In a then selected subset, we found after further detailed diagnostic interviews one Bengali female student with visual agnosia for face recognition only. Several other members of her large family reported the same impairment of face recognition. The segregation pattern of PA in this family is also compatible with autosomal-dominant inheritance.
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Affiliation(s)
- Ingo Kennerknecht
- Institut für Humangenetik, Westfälische Wilhelms Universität, Münster, Germany.
| | - Nina Plümpe
- Institut für Humangenetik, Westfälische Wilhelms Universität, Münster, Germany
| | - Steve Edwards
- Department of Psychology, Zululand University, P. Bag X1001, KwaDlangezwa, 3886, South Africa
| | - Rajiva Raman
- Department of Zoology and Molecular and Human Genetics, Banaras Hindu University, Varanasi, 221005, India
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Endicott P, Metspalu M, Stringer C, Macaulay V, Cooper A, Sanchez JJ. Multiplexed SNP typing of ancient DNA clarifies the origin of Andaman mtDNA haplogroups amongst South Asian tribal populations. PLoS One 2006; 1:e81. [PMID: 17218991 PMCID: PMC1766372 DOI: 10.1371/journal.pone.0000081] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2006] [Accepted: 10/30/2006] [Indexed: 11/18/2022] Open
Abstract
The issue of errors in genetic data sets is of growing concern, particularly in population genetics where whole genome mtDNA sequence data is coming under increased scrutiny. Multiplexed PCR reactions, combined with SNP typing, are currently under-exploited in this context, but have the potential to genotype whole populations rapidly and accurately, significantly reducing the amount of errors appearing in published data sets. To show the sensitivity of this technique for screening mtDNA genomic sequence data, 20 historic samples of the enigmatic Andaman Islanders and 12 modern samples from three Indian tribal populations (Chenchu, Lambadi and Lodha) were genotyped for 20 coding region sites after provisional haplogroup assignment with control region sequences. The genotype data from the historic samples significantly revise the topologies for the Andaman M31 and M32 mtDNA lineages by rectifying conflicts in published data sets. The new Indian data extend the distribution of the M31a lineage to South Asia, challenging previous interpretations of mtDNA phylogeography. This genetic connection between the ancestors of the Andamanese and South Asian tribal groups approximately 30 kya has important implications for the debate concerning migration routes and settlement patterns of humans leaving Africa during the late Pleistocene, and indicates the need for more detailed genotyping strategies. The methodology serves as a low-cost, high-throughput model for the production and authentication of data from modern or ancient DNA, and demonstrates the value of museum collections as important records of human genetic diversity.
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Affiliation(s)
- Phillip Endicott
- Department of Zoology, University of Oxford Oxford, United Kingdom.
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165
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Roostalu U, Kutuev I, Loogväli EL, Metspalu E, Tambets K, Reidla M, Khusnutdinova EK, Usanga E, Kivisild T, Villems R. Origin and expansion of haplogroup H, the dominant human mitochondrial DNA lineage in West Eurasia: the Near Eastern and Caucasian perspective. Mol Biol Evol 2006; 24:436-48. [PMID: 17099056 DOI: 10.1093/molbev/msl173] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
More than a third of the European pool of human mitochondrial DNA (mtDNA) is fragmented into a number of subclades of haplogroup (hg) H, the most frequent hg throughout western Eurasia. Although there has been considerable recent progress in studying mitochondrial genome variation in Europe at the complete sequence resolution, little data of comparable resolution is so far available for regions like the Caucasus and the Near and Middle East-areas where most of European genetic lineages, including hg H, have likely emerged. This gap in our knowledge causes a serious hindrance for progress in understanding the demographic prehistory of Europe and western Eurasia in general. Here we describe the phylogeography of hg H in the populations of the Near East and the Caucasus. We have analyzed 545 samples of hg H at high resolution, including 15 novel complete mtDNA sequences. As in Europe, most of the present-day Near Eastern-Caucasus area variants of hg H started to expand after the last glacial maximum (LGM) and presumably before the Holocene. Yet importantly, several hg H subclades in Near East and Southern Caucasus region coalesce to the pre-LGM period. Furthermore, irrespective of their common origin, significant differences between the distribution of hg H sub-hgs in Europe and in the Near East and South Caucasus imply limited post-LGM maternal gene flow between these regions. In a contrast, the North Caucasus mitochondrial gene pool has received an influx of hg H variants, arriving from the Ponto-Caspian/East European area.
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Affiliation(s)
- U Roostalu
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
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166
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Sahoo S, Kashyap VK. Phylogeography of mitochondrial DNA and Y-chromosome haplogroups reveal asymmetric gene flow in populations of Eastern India. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 131:84-97. [PMID: 16485297 DOI: 10.1002/ajpa.20399] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Polymorphisms in mitochondrial (mt) DNA and Y-chromosomes of seven socially and linguistically diverse castes and tribes of Eastern India were examined to determine their genetic relationships, their origin, and the influence of demographic factors on population structure. Samples from the Orissa Brahmin, Karan, Khandayat, Gope, Juang, Saora, and Paroja were analyzed for mtDNA hypervariable sequence (HVS) I and II, eight Y-chromosome short tandem repeats (Y-STRs), and lineage-defining mutations diagnostic for Indian- and Eurasian-specific haplogroups. Our results reveal that haplotype diversity and mean pairwise differences (MPD) was higher in caste groups of the region (>0.998, for both systems) compared to tribes (0.917-0.996 for Y-STRs, and 0.958-0.988 for mtDNA haplotypes). The majority of paternal lineages belong to the R1a1, O2a, and H haplogroups (62.7%), while 73.2% of maternal lineages comprise the Indian-specific M*, M5, M30, and R* mtDNA haplogroups, with a sporadic occurrence of West Eurasian lineages. Our study reveals that Orissa Brahmins (a higher caste population) have a genetic affinity with Indo-European speakers of Eastern Europe, although the Y-chromosome data show that the genetic distances of populations are not correlated to their position in the caste hierarchy. The high frequency of the O2a haplogroup and absence of East Asian-specific mtDNA lineages in the Juang and Saora suggest that a migration of Austro-Asiatic tribes to mainland India was exclusively male-mediated which occurred during the demographic expansion of Neolithic farmers in southern China. The phylogeographic analysis of mtDNA and Y-chromosomes revealed varied ancestral sources for the diverse genetic components of the populations of Eastern India.
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Affiliation(s)
- Sanghamitra Sahoo
- National DNA Analysis Centre, Central Forensic Science Laboratory, Kolkata 700 014, India
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167
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Zerjal T, Pandya A, Thangaraj K, Ling EYS, Kearley J, Bertoneri S, Paracchini S, Singh L, Tyler-Smith C. Y-chromosomal insights into the genetic impact of the caste system in India. Hum Genet 2006; 121:137-44. [PMID: 17075717 PMCID: PMC2590678 DOI: 10.1007/s00439-006-0282-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 10/11/2006] [Indexed: 11/29/2022]
Abstract
The caste system has persisted in Indian Hindu society for around 3,500 years. Like the Y chromosome, caste is defined at birth, and males cannot change their caste. In order to investigate the genetic consequences of this system, we have analysed male-lineage variation in a sample of 227 Indian men of known caste, 141 from the Jaunpur district of Uttar Pradesh and 86 from the rest of India. We typed 131 Y-chromosomal binary markers and 16 microsatellites. We find striking evidence for male substructure: in particular, Brahmins and Kshatriyas (but not other castes) from Jaunpur each show low diversity and the predominance of a single distinct cluster of haplotypes. These findings confirm the genetic isolation and drift within the Jaunpur upper castes, which are likely to result from founder effects and social factors. In the other castes, there may be either larger effective population sizes, or less strict isolation, or both.
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Affiliation(s)
- Tatiana Zerjal
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Arpita Pandya
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | | | | | - Lalji Singh
- Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Department of Biochemistry, University of Oxford, Oxford, UK
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168
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van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM. Mitochondrial genomics identifies major haplogroups in Aboriginal Australians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2006; 131:282-94. [PMID: 16596590 DOI: 10.1002/ajpa.20426] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.
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Affiliation(s)
- Sheila M van Holst Pellekaan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, New South Wales 2052, Australia.
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169
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Barnabas S, Shouche Y, Suresh CG. High-resolution mtDNA studies of the Indian population: implications for palaeolithic settlement of the Indian subcontinent. Ann Hum Genet 2006; 70:42-58. [PMID: 16441256 DOI: 10.1111/j.1529-8817.2005.00207.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The population of the Indian subcontinent represents a very complex social and cultural structure. Occupying a geographically central position for the early modern human migrations, indications are that the founder group that migrated out of East Africa also reached India. In the present study we used the twin strategy of mapping the whole mitochondrial DNA (mtDNA) using the standard 14 restriction enzymes, and sequencing the non-transcribed HVSI region, to derive maximum maternal lineages from a sample of non-tribal Indians. The essential features of the reduced median network of the two datasets were the same. Both showed two demographic expansions of two major haplogroups, 'M' and 'N'. The reduced median network was drawn with inputs from other studies on the Indian population, and correlated with data from other ethnic populations. The coalescence time of expansions and genetic diversity were estimated. A reduced median network was also drawn combining data from studies on Africans, Southeast Asians and West-Eurasians, tracing the migration of 'M' from East Africa to India. A time estimate of the migration of major mtDNA haplogroups from Africa was attempted. The comparison of a set of Indian maternal lineages belonging to different geographical regions of the country, with other populations revealed the in-situ differentiation and antiquity of the Indian population. Our analysis places the 'southern route' migration as the source of haplogroup 'M'. Multiple migrations might have brought the other major haplogroups, 'N' and 'R', found in our sample to India. Archaeological evidence of modern humans in the subcontinent supports this mtDNA study.
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Affiliation(s)
- S Barnabas
- Division of Biochemical Sciences, National Chemical Laboratory, Pune 411008, India.
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170
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Gutala R, Carvalho-Silva DR, Jin L, Yngvadottir B, Avadhanula V, Nanne K, Singh L, Chakraborty R, Tyler-Smith C. A shared Y-chromosomal heritage between Muslims and Hindus in India. Hum Genet 2006; 120:543-51. [PMID: 16951948 PMCID: PMC2590854 DOI: 10.1007/s00439-006-0234-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2006] [Accepted: 07/12/2006] [Indexed: 11/28/2022]
Abstract
Arab forces conquered the Indus Delta region in 711 AD: and, although a Muslim state was established there, their influence was barely felt in the rest of South Asia at that time. By the end of the tenth century, Central Asian Muslims moved into India from the northwest and expanded throughout the subcontinent. Muslim communities are now the largest minority religion in India, comprising more than 138 million people in a predominantly Hindu population of over one billion. It is unclear whether the Muslim expansion in India was a purely cultural phenomenon or had a genetic impact on the local population. To address this question from a male perspective, we typed eight microsatellite loci and 16 binary markers from the Y chromosome in 246 Muslims from Andhra Pradesh, and compared them to published data on 4,204 males from East Asia, Central Asia, other parts of India, Sri Lanka, Pakistan, Iran, the Middle East, Turkey, Egypt and Morocco. We find that the Muslim populations in general are genetically closer to their non-Muslim geographical neighbors than to other Muslims in India, and that there is a highly significant correlation between genetics and geography (but not religion). Our findings indicate that, despite the documented practice of marriage between Muslim men and Hindu women, Islamization in India did not involve large-scale replacement of Hindu Y chromosomes. The Muslim expansion in India was predominantly a cultural change and was not accompanied by significant gene flow, as seen in other places, such as China and Central Asia.
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Affiliation(s)
- Ramana Gutala
- Department of Medicine, University of Texas Health Science Center, San Antonio, USA
| | | | - Li Jin
- Center for Genome information, University of Cincinnati, Cincinnati, USA
| | | | | | - Khaja Nanne
- Deccan College of Medical Sciences, Hyderabad, India
| | - Lalji Singh
- Center for Cellular and Molecular Biology, Hyderabad, India
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171
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Thanseem I, Thangaraj K, Chaubey G, Singh VK, Bhaskar LVKS, Reddy BM, Reddy AG, Singh L. Genetic affinities among the lower castes and tribal groups of India: inference from Y chromosome and mitochondrial DNA. BMC Genet 2006; 7:42. [PMID: 16893451 PMCID: PMC1569435 DOI: 10.1186/1471-2156-7-42] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Accepted: 08/07/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND India is a country with enormous social and cultural diversity due to its positioning on the crossroads of many historic and pre-historic human migrations. The hierarchical caste system in the Hindu society dominates the social structure of the Indian populations. The origin of the caste system in India is a matter of debate with many linguists and anthropologists suggesting that it began with the arrival of Indo-European speakers from Central Asia about 3500 years ago. Previous genetic studies based on Indian populations failed to achieve a consensus in this regard. We analysed the Y-chromosome and mitochondrial DNA of three tribal populations of southern India, compared the results with available data from the Indian subcontinent and tried to reconstruct the evolutionary history of Indian caste and tribal populations. RESULTS No significant difference was observed in the mitochondrial DNA between Indian tribal and caste populations, except for the presence of a higher frequency of west Eurasian-specific haplogroups in the higher castes, mostly in the north western part of India. On the other hand, the study of the Indian Y lineages revealed distinct distribution patterns among caste and tribal populations. The paternal lineages of Indian lower castes showed significantly closer affinity to the tribal populations than to the upper castes. The frequencies of deep-rooted Y haplogroups such as M89, M52, and M95 were higher in the lower castes and tribes, compared to the upper castes. CONCLUSION The present study suggests that the vast majority (> 98%) of the Indian maternal gene pool, consisting of Indio-European and Dravidian speakers, is genetically more or less uniform. Invasions after the late Pleistocene settlement might have been mostly male-mediated. However, Y-SNP data provides compelling genetic evidence for a tribal origin of the lower caste populations in the subcontinent. Lower caste groups might have originated with the hierarchical divisions that arose within the tribal groups with the spread of Neolithic agriculturalists, much earlier than the arrival of Aryan speakers. The Indo-Europeans established themselves as upper castes among this already developed caste-like class structure within the tribes.
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Affiliation(s)
- Ismail Thanseem
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India
| | - Kumarasamy Thangaraj
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India
| | - Gyaneshwer Chaubey
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India
- Estonian Biocentre, Riia, 23, Tartu- 51010, Estonia
| | - Vijay Kumar Singh
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India
| | | | - B Mohan Reddy
- Biological Anthropology Unit, Indian Statistical Research Institute, Habsiguda, Hyderabad, India
| | - Alla G Reddy
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India
| | - Lalji Singh
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad- 500 007, India
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172
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Malyarchuk BA, Grzybowski T, Derenko MV, Czarny J, Miścicka-Sliwka D. Mitochondrial DNA diversity in the Polish Roma. Ann Hum Genet 2006; 70:195-206. [PMID: 16626330 DOI: 10.1111/j.1529-8817.2005.00222.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondrial DNA variability in the Polish Roma population has been studied by means of hypervariable segment I and II (HVS I and II) sequencing and restriction fragment-length polymorphism analysis of the mtDNA coding region. The mtDNA haplotypes detected in the Polish Roma fall into the common Eurasian mitochondrial haplogroups (H, U3, K, J1, X, I, W, and M*). The results of complete mtDNA sequencing clearly indicate that the Romani M*-lineage belongs to the Indian-specific haplogroup M5, which is characterized by three transitions in the coding region, at sites 12477, 3921 and 709. Molecular variance analysis inferred from mtDNA data reveals that genetic distances between the Roma groups are considerably larger than those between the surrounding European populations. Also, there are significant differences between the Bulgarian Roma (Balkan and Vlax groups) and West European Roma (Polish, Lithuanian and Spanish groups). Comparative analysis of mtDNA haplotypes in the Roma populations shows that different haplotypes appear to demonstrate impressive founder effects: M5 and H (16261-16304) in all Romani groups; U3, I and J1 in some Romani groups. Interestingly, haplogroup K (with HVS I motif 16224-16234-16311) found in the Polish Roma sample seems to be specific for Ashkenazi Jewish populations.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, 685000 Magadan, Russia.
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173
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Beleza S, Gusmão L, Lopes A, Alves C, Gomes I, Giouzeli M, Calafell F, Carracedo A, Amorim A. Micro-phylogeographic and demographic history of Portuguese male lineages. Ann Hum Genet 2006; 70:181-94. [PMID: 16626329 DOI: 10.1111/j.1529-8817.2005.00221.x] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The clinal pattern observed for the distribution of Y-chromosome lineages in Europe is not always reflected at a geographically smaller scale. Six hundred and sixty-three male samples from the 18 administrative districts of Portugal were typed for 25 Y-chromosome biallelic and 15 microsatellite markers, in order to assess the degree of substructuring of male lineage distribution. Haplogroup frequency distributions, Analysis of Molecular Variance (AMOVA) and genetic distance analyses at both Y-SNP and Y-STR levels revealed a general genetic homogeneity of Portuguese sub-populations. The traditional division of the country in north, central and south, which is usually considered in studies addressing questions of the genetic variation distribution in Portugal, was not reflected in the Y-haplotype distribution. Instead, just one sub-region (Alentejo) stood out due to the presence of high diversity levels and a higher number of different lineages, at higher frequencies than in other regions. These results are reconciled with the historical evidence available, assuming that from prehistorical times down to the end of the medieval period this region harboured the most diverse groups of people and, because of economic depression, remained relatively isolated from recent homogenisation movements. The finding of a broadly homogeneous background for the Portuguese population has vast repercussions in forensic, epidemiological and association studies.
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Affiliation(s)
- Sandra Beleza
- Instituto de Patologia e Imunologia da Universidade do Porto (IPATIMUP), Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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174
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Thangaraj K, Chaubey G, Singh VK, Vanniarajan A, Thanseem I, Reddy AG, Singh L. In situ origin of deep rooting lineages of mitochondrial Macrohaplogroup 'M' in India. BMC Genomics 2006; 7:151. [PMID: 16776823 PMCID: PMC1534032 DOI: 10.1186/1471-2164-7-151] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2005] [Accepted: 06/15/2006] [Indexed: 11/18/2022] Open
Abstract
Background Macrohaplogroups 'M' and 'N' have evolved almost in parallel from a founder haplogroup L3. Macrohaplogroup N in India has already been defined in previous studies and recently the macrohaplogroup M among the Indian populations has been characterized. In this study, we attempted to reconstruct and re-evaluate the phylogeny of Macrohaplogroup M, which harbors more than 60% of the Indian mtDNA lineage, and to shed light on the origin of its deep rooting haplogroups. Results Using 11 whole mtDNA and 2231 partial coding sequence of Indian M lineage selected from 8670 HVS1 sequences across India, we have reconstructed the tree including Andamanese-specific lineage M31 and calculated the time depth of all the nodes. We defined one novel haplogroup M41, and revised the classification of haplogroups M3, M18, and M31. Conclusion Our result indicates that the Indian mtDNA pool consists of several deep rooting lineages of macrohaplogroup 'M' suggesting in-situ origin of these haplogroups in South Asia, most likely in the India. These deep rooting lineages are not language specific and spread over all the language groups in India. Moreover, our reanalysis of the Andamanese-specific lineage M31 suggests population specific two clear-cut subclades (M31a1 and M31a2). Onge and Jarwa share M31a1 branch while M31a2 clade is present in only Great Andamanese individuals. Overall our study supported the one wave, rapid dispersal theory of modern humans along the Asian coast.
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Affiliation(s)
| | - Gyaneshwer Chaubey
- Centre for Cellular and Molecular Biology, Hyderabad-500 007, India
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu and Estonian Biocentre, Tartu, Estonia
| | | | | | - Ismail Thanseem
- Centre for Cellular and Molecular Biology, Hyderabad-500 007, India
| | - Alla G Reddy
- Centre for Cellular and Molecular Biology, Hyderabad-500 007, India
| | - Lalji Singh
- Centre for Cellular and Molecular Biology, Hyderabad-500 007, India
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175
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Regueiro M, Cadenas AM, Gayden T, Underhill PA, Herrera RJ. Iran: tricontinental nexus for Y-chromosome driven migration. Hum Hered 2006; 61:132-43. [PMID: 16770078 DOI: 10.1159/000093774] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2005] [Accepted: 03/23/2006] [Indexed: 11/19/2022] Open
Abstract
Due to its pivotal geographic position, present day Iran likely served as a gateway of reciprocal human movements. However, the extent to which the deserts within the Iranian plateau and the mountain ranges surrounding Persia inhibited gene flow via this corridor remains uncertain. In order to assess the magnitude of this region's role as a nexus for Africa, Asia and Europe in human migrations, high-resolution Y-chromosome analyses were performed on 150 Iranian males. Haplogroup data were subsequently compared to regional populations characterized at similar phylogenetic levels. The Iranians display considerable haplogroup diversity consistent with patterns observed in populations of the Middle East overall, reinforcing the notion of Persia as a venue for human disseminations. Admixture analyses of geographically targeted, regional populations along the latitudinal corridor spanning from Anatolia to the Indus Valley demonstrated contributions to Persia from both the east and west. However, significant differences were uncovered upon stratification of the gene donors, including higher proportions from central east and southeast Turkey as compared to Pakistan. In addition to the modulating effects of geographic obstacles, culturally mediated amalgamations consistent with the diverse spectrum of a variety of historical empires may account for the distribution of haplogroups and lineages observed. Our study of high-resolution Y-chromosome genotyping allowed for an in-depth analysis unattained in previous studies of the area, revealing important migratory and demographic events that shaped the contemporary genetic landscape.
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Affiliation(s)
- M Regueiro
- Department of Biological Sciences, Florida International University, University Park, OE 304, Miami, FL 33199, USA
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176
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177
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Kashyap VK, Guha S, Sitalaximi T, Bindu GH, Hasnain SE, Trivedi R. Genetic structure of Indian populations based on fifteen autosomal microsatellite loci. BMC Genet 2006; 7:28. [PMID: 16707019 PMCID: PMC1513393 DOI: 10.1186/1471-2156-7-28] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2005] [Accepted: 05/17/2006] [Indexed: 11/21/2022] Open
Abstract
Background Indian populations endowed with unparalleled genetic complexity have received a great deal of attention from scientists world over. However, the fundamental question over their ancestry, whether they are all genetically similar or do exhibit differences attributable to ethnicity, language, geography or socio-cultural affiliation is still unresolved. In order to decipher their underlying genetic structure, we undertook a study on 3522 individuals belonging to 54 endogamous Indian populations representing all major ethnic, linguistic and geographic groups and assessed the genetic variation using autosomal microsatellite markers. Results The distribution of the most frequent allele was uniform across populations, revealing an underlying genetic similarity. Patterns of allele distribution suggestive of ethnic or geographic propinquity were discernible only in a few of the populations and was not applicable to the entire dataset while a number of the populations exhibited distinct identities evident from the occurrence of unique alleles in them. Genetic substructuring was detected among populations originating from northeastern and southern India reflective of their migrational histories and genetic isolation respectively. Conclusion Our analyses based on autosomal microsatellite markers detected no evidence of general clustering of population groups based on ethnic, linguistic, geographic or socio-cultural affiliations. The existence of substructuring in populations from northeastern and southern India has notable implications for population genetic studies and forensic databases where broad grouping of populations based on such affiliations are frequently employed.
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Affiliation(s)
- VK Kashyap
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata 700014, West Bengal, India
- National Institute of Biologicals, A-32, Sector 62, Institutional Area, Noida 201307, Uttar Pradesh, India
| | - Saurav Guha
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata 700014, West Bengal, India
| | - T Sitalaximi
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata 700014, West Bengal, India
| | - G Hima Bindu
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata 700014, West Bengal, India
| | - Seyed E Hasnain
- Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500076, Andhra Pradesh, India
| | - R Trivedi
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata 700014, West Bengal, India
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178
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Shepard EM, Herrera RJ. Iranian STR variation at the fringes of biogeographical demarcation. Forensic Sci Int 2006; 158:140-8. [PMID: 15998573 DOI: 10.1016/j.forsciint.2005.05.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2005] [Revised: 05/10/2005] [Accepted: 05/10/2005] [Indexed: 11/26/2022]
Abstract
The integrative relationship between population genetics and forensic biology allows for a thorough genetic characterization of extant human populations. This study aimed to genetically characterize 150 unrelated healthy donors from a general population in Iran both forensically and phylogenetically. The allelic frequencies of 15 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818 and FGA) were generated. This constitutes the core of polymerase chain reaction (PCR)-based DNA genetic markers in the US Combined DNA Index System (CODIS) plus two additional loci (D2S1338 and D19S433) that together are consistent with several other worldwide database requirements. There were no deviations from Hardy-Weinberg expectations. Based upon the allelic frequencies, several important forensic parameters were calculated including: gene diversity (GD) index, power of discrimination (PD), polymorphic information content (PIC) and power of exclusion (PE). G-tests indicate the allelic frequencies of the Iranians are statistically non-significant compared to two Turkish populations yet, statistically different from the remaining 18 groups obtained from the literature and examined in this study. This suggests that the Iranian dataset may be forensically equivalent to the dataset from the Turkish region of Eastern Anatolia and the general population from Turkey. Phylogenetic analysis of our population with the full set of 15 loci indicate the Iranians occupy an intermediate position relative to the major Caucasian and East Asian clades on a global level. A regional phylogenetic analysis using 13 of the 15 loci indicate the Iranians segregate in a more compact association with groups from southeastern Spain, Arabs from Morocco and Syria, and especially with the general population from Turkey and those from Eastern Anatolia. These groups are flanked by highly differentiated populations from northern India and a Berber group from Tunisia on opposing ends of the regional phylogram. This report also demonstrates the necessity to thoroughly characterize the genetic composition of populations located in geographic intersections in order to choose the appropriate dataset on which to base forensic calculations, not only at an intra-population level, but also at an inter-population level as well.
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Affiliation(s)
- E M Shepard
- Department of Biological Sciences, Florida International University, University Park, OE 304, Miami, FL 33199, USA
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Thangaraj K, Chaubey G, Singh VK, Reddy AG, Pavate PP, Singh L. Genetic profile of nine autosomal STR loci among Halakki and Kunabhi populations of Karnataka, India. J Forensic Sci 2006; 51:190-2. [PMID: 16423250 DOI: 10.1111/j.1556-4029.2005.00038.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
POPULATION Blood samples were collected from a total of 84 healthy and unrelated Halakki (44) and Kunabhi (40) populations, with their informed written consent. The geographic location of the sampled area is shown in Fig. 1. Both the populations are endogamous, and they belong to Dravidian linguistic family. Halakki is a tribal group having a population size of approximately 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, who are approximately 35,214 in number. The male Kunabhi can be identified by their tattoo marks. A necklace is the symbol of married women. They were hunters and gatherers, but at present they practice agriculture.
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180
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Trivedi R, Sitalaximi T, Banerjee J, Singh A, Sircar PK, Kashyap VK. Molecular insights into the origins of the Shompen, a declining population of the Nicobar archipelago. J Hum Genet 2006; 51:217-226. [PMID: 16453062 DOI: 10.1007/s10038-005-0349-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2005] [Accepted: 11/07/2005] [Indexed: 10/25/2022]
Abstract
The Shompen, one of the most isolated and poorly understood contemporary hunter-gatherer populations, inhabit Great Nicobar Island, the southernmost island of the Nicobar archipelago. Morphological imprints in the Shompen were interpreted to favour a mixed Indo-Chinese, Malay, Negrito and Dravidian origin. Analyses of the mitochondrial, Y-chromosomal and autosomal gene pool of contemporary Shompen have revealed low diversity, illustrating a founder effect in the island population. Mitochondrial sequence analyses revealed the presence of two haplogroups of R lineage: B5a, and a newly defined clade, R12. Y-chromosomal analyses demonstrated the occurrence of a single lineage found predominantly in Austro-Asiatic speakers across Asia. With the different types of genetic markers analysed, the Shompen exhibit varying levels of genetic relatedness with the Nicobarese, and Austro-Asiatic speakers of mainland India and Southeast Asia. These genetic analyses provide evidence that the Shompen, an offshoot of the Nicobarese, are descendants of Mesolithic hunter-gatherers of Southeast Asian origin, deriving from at least two source populations.
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Affiliation(s)
- Rajni Trivedi
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata, 700014, West Bengal, India
| | - T Sitalaximi
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata, 700014, West Bengal, India
| | - Jheelam Banerjee
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata, 700014, West Bengal, India
| | - Anamika Singh
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata, 700014, West Bengal, India
| | - P K Sircar
- Andaman Adim Janjati Vikas Samiti, Government of India, Port Blair, India
| | - V K Kashyap
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata, 700014, West Bengal, India.
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181
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Sengupta S, Zhivotovsky LA, King R, Mehdi SQ, Edmonds CA, Chow CET, Lin AA, Mitra M, Sil SK, Ramesh A, Usha Rani MV, Thakur CM, Cavalli-Sforza LL, Majumder PP, Underhill PA. Polarity and temporality of high-resolution y-chromosome distributions in India identify both indigenous and exogenous expansions and reveal minor genetic influence of Central Asian pastoralists. Am J Hum Genet 2006; 78:202-21. [PMID: 16400607 PMCID: PMC1380230 DOI: 10.1086/499411] [Citation(s) in RCA: 283] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 11/03/2005] [Indexed: 11/03/2022] Open
Abstract
Although considerable cultural impact on social hierarchy and language in South Asia is attributable to the arrival of nomadic Central Asian pastoralists, genetic data (mitochondrial and Y chromosomal) have yielded dramatically conflicting inferences on the genetic origins of tribes and castes of South Asia. We sought to resolve this conflict, using high-resolution data on 69 informative Y-chromosome binary markers and 10 microsatellite markers from a large set of geographically, socially, and linguistically representative ethnic groups of South Asia. We found that the influence of Central Asia on the pre-existing gene pool was minor. The ages of accumulated microsatellite variation in the majority of Indian haplogroups exceed 10,000-15,000 years, which attests to the antiquity of regional differentiation. Therefore, our data do not support models that invoke a pronounced recent genetic input from Central Asia to explain the observed genetic variation in South Asia. R1a1 and R2 haplogroups indicate demographic complexity that is inconsistent with a recent single history. Associated microsatellite analyses of the high-frequency R1a1 haplogroup chromosomes indicate independent recent histories of the Indus Valley and the peninsular Indian region. Our data are also more consistent with a peninsular origin of Dravidian speakers than a source with proximity to the Indus and with significant genetic input resulting from demic diffusion associated with agriculture. Our results underscore the importance of marker ascertainment for distinguishing phylogenetic terminal branches from basal nodes when attributing ancestral composition and temporality to either indigenous or exogenous sources. Our reappraisal indicates that pre-Holocene and Holocene-era--not Indo-European--expansions have shaped the distinctive South Asian Y-chromosome landscape.
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Affiliation(s)
- Sanghamitra Sengupta
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Lev A. Zhivotovsky
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Roy King
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - S. Q. Mehdi
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Christopher A. Edmonds
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Cheryl-Emiliane T. Chow
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Alice A. Lin
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Mitashree Mitra
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Samir K. Sil
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - A. Ramesh
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - M. V. Usha Rani
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Chitra M. Thakur
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - L. Luca Cavalli-Sforza
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Partha P. Majumder
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
| | - Peter A. Underhill
- Human Genetics Unit, Indian Statistical Institute, Kolkata, India; N. I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow; Department of Genetics, Stanford University, Stanford; Biomedical and Genetic Engineering Division, Dr. A. Q. Khan Research Laboratories, Islamabad; School of Studies in Anthropology, Pandit Ravishankar Shukla University, Raipur, India; University of Tripura, Tripura, India; Department of Genetics, University of Madras, Chennai, India; Department of Environmental Sciences, Bharathiar University, Coimbatore, India; and B. J. Wadia Hospital for Children, Mumbai, India
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182
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Sahoo S, Singh A, Himabindu G, Banerjee J, Sitalaximi T, Gaikwad S, Trivedi R, Endicott P, Kivisild T, Metspalu M, Villems R, Kashyap VK. A prehistory of Indian Y chromosomes: evaluating demic diffusion scenarios. Proc Natl Acad Sci U S A 2006; 103:843-8. [PMID: 16415161 PMCID: PMC1347984 DOI: 10.1073/pnas.0507714103] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic origins and demographic history of Indian populations is important both for questions concerning the early settlement of Eurasia and more recent events, including the appearance of Indo-Aryan languages and settled agriculture in the subcontinent. Although there is general agreement that Indian caste and tribal populations share a common late Pleistocene maternal ancestry in India, some studies of the Y-chromosome markers have suggested a recent, substantial incursion from Central or West Eurasia. To investigate the origin of paternal lineages of Indian populations, 936 Y chromosomes, representing 32 tribal and 45 caste groups from all four major linguistic groups of India, were analyzed for 38 single-nucleotide polymorphic markers. Phylogeography of the major Y-chromosomal haplogroups in India, genetic distance, and admixture analyses all indicate that the recent external contribution to Dravidian- and Hindi-speaking caste groups has been low. The sharing of some Y-chromosomal haplogroups between Indian and Central Asian populations is most parsimoniously explained by a deep, common ancestry between the two regions, with diffusion of some Indian-specific lineages northward. The Y-chromosomal data consistently suggest a largely South Asian origin for Indian caste communities and therefore argue against any major influx, from regions north and west of India, of people associated either with the development of agriculture or the spread of the Indo-Aryan language family. The dyadic Y-chromosome composition of Tibeto-Burman speakers of India, however, can be attributed to a recent demographic process, which appears to have absorbed and overlain populations who previously spoke Austro-Asiatic languages.
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Affiliation(s)
- Sanghamitra Sahoo
- National DNA Analysis Centre, Central Forensic Science Laboratory, Kolkata 700014, India
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183
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Excavating the mitochondrial genome identifies major haplogroups in Aboriginal Australians. ACTA ACUST UNITED AC 2006. [DOI: 10.3828/bfarm.2006.1.3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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184
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Kumar V, Langsiteh BT, Biswas S, Babu JP, Rao TN, Thangaraj K, Reddy AG, Singh L, Reddy BM. Asian and non-Asian origins of Mon-Khmer- and Mundari-speaking Austro-Asiatic populations of India. Am J Hum Biol 2006; 18:461-9. [PMID: 16788903 DOI: 10.1002/ajhb.20512] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In the present study, we analyzed 1,686 samples from 31 tribal populations of India for the mitochondrial DNA 9-base-pair deletion/insertion polymorphism, and characterized them based on the relevant mitochondrial DNA coding-region single nucleotide polymorphisms and hypervariable region I motifs, to test the genetic origins of the ethnically and linguistically heterogeneous Austro-Asiatic tribes of India. A comparative analysis of our results with the existing data suggests multiple origins of Austro-Asiatic tribes in India, and particularly the Asian and non-Asian origins of the Mon-Khmer and the Mundari populations. We also identified a novel subclade of haplogroup B in the Mon-Khmer Khasi tribes that distinguishes them from the Nicobarese, indicating two different waves of migration of the Mon-Khmer tribes in India.
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Affiliation(s)
- Vikrant Kumar
- Biological Anthropolgy Unit, Indian Statistical Institute, Habsiguda, Hyderabad 500 007, India
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185
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Sun C, Kong QP, Palanichamy MG, Agrawal S, Bandelt HJ, Yao YG, Khan F, Zhu CL, Chaudhuri TK, Zhang YP. The dazzling array of basal branches in the mtDNA macrohaplogroup M from India as inferred from complete genomes. Mol Biol Evol 2005; 23:683-90. [PMID: 16361303 DOI: 10.1093/molbev/msj078] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Many efforts based on complete mitochondrial DNA (mtDNA) genomes have been made to depict the global mtDNA landscape, but the phylogeny of Indian macrohaplogroup M has not yet been resolved in detail. To fill this lacuna, we took the same strategy as in our recent analysis of Indian mtDNA macrohaplogroup N and selected 56 mtDNAs from over 1,200 samples across India for complete sequencing, with the intention to cover all Indian autochthonous M lineages. As a result, the phylogenetic status of previously identified haplogroups based on control-region and/or partial coding-region information, such as M2, M3, M4, M5, M6, M30, and M33, was solidified or redefined here. Moreover, seven novel basal M haplogroups (viz., M34-M40) were identified, and yet another five singular branches of the M phylogeny were discovered in the present study. The comparison of matrilineal components among India, East Asia, Southeast Asia, and Oceania at the deepest level yielded a star-like and nonoverlapping pattern, reflecting a rapid mode of modern human dispersal along the Asian coast after the initial "out-of-Africa" event.
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Affiliation(s)
- Chang Sun
- Laboratory of Cellular and Molecular Evolution, and Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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186
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Watkins WS, Prasad BVR, Naidu JM, Rao BB, Bhanu BA, Ramachandran B, Das PK, Gai PB, Reddy PC, Reddy PG, Sethuraman M, Bamshad MJ, Jorde LB. Diversity and divergence among the tribal populations of India. Ann Hum Genet 2005; 69:680-92. [PMID: 16266407 DOI: 10.1046/j.1529-8817.2005.00200.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Tribal populations of the Indian subcontinent have been of longstanding interest to anthropologists and human geneticists. To investigate the relationship of Indian tribes to Indian castes and continental populations, we analyzed 45 unlinked autosomal STR loci in 9 tribal groups, 8 castes, and 18 populations from Africa, Europe and East Asia. South Indian tribal populations demonstrate low within-population heterozygosity (range: 0.54 - 0.69), while tribal populations sampled further north and east have higher heterozygosity (range: 0.69 - 0.74). Genetic distance estimates show that tribal Indians are more closely related to caste Indians than to other major groups. Between-tribe differentiation is high and exceeds that for eight sub-Saharan African populations (4.8% vs. 3.7%). Telugu-speaking populations are less differentiated than non-Telugu speakers (F(ST): 0.029 vs. 0.079), but geographic distance was not predictive of genetic affinity between tribes. South Indian tribes show significant population structure, and individuals can be clustered statistically into groups that correspond with their tribal affiliation. These results are consistent with high levels of genetic drift and isolation in Indian tribal populations, particularly those of South India, and they imply that these populations may be potential candidates for linkage disequilibrium and association mapping.
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Affiliation(s)
- W S Watkins
- Department of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.
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187
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James H, Petraglia M. Modern Human Origins and the Evolution of Behavior in the Later Pleistocene Record of South Asia. CURRENT ANTHROPOLOGY 2005. [DOI: 10.1086/444365] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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188
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Kalaydjieva L, Morar B, Chaix R, Tang H. A newly discovered founder population: the Roma/Gypsies. Bioessays 2005; 27:1084-94. [PMID: 16163730 DOI: 10.1002/bies.20287] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The Gypsies (a misnomer, derived from an early legend about Egyptian origins) defy the conventional definition of a population: they have no nation-state, speak different languages, belong to many religions and comprise a mosaic of socially and culturally divergent groups separated by strict rules of endogamy. Referred to as "the invisible minority", the Gypsies have for centuries been ignored by Western medicine, and their genetic heritage has only recently attracted attention. Common origins from a small group of ancestors characterise the 8-10 million European Gypsies as an unusual trans-national founder population, whose exodus from India played the role of a profound demographic bottleneck. Social and economic pressures within Europe led to gradual fragmentation, generating multiple genetically differentiated subisolates. The string of population bottlenecks and founder effects have shaped a unique genetic profile, whose potential for genetic research can be met only by study designs that acknowledge cultural tradition and self-identity.
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Affiliation(s)
- Luba Kalaydjieva
- Western Australian Institute for Medical Research and Centre for Medical Research, The University of Western Australia, Nedlands, Perth, Australia.
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189
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Sharma S, Saha A, Rai E, Bhat A, Bamezai R. Human mtDNA hypervariable regions, HVR I and II, hint at deep common maternal founder and subsequent maternal gene flow in Indian population groups. J Hum Genet 2005; 50:497-506. [PMID: 16205836 DOI: 10.1007/s10038-005-0284-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2005] [Accepted: 07/21/2005] [Indexed: 10/25/2022]
Abstract
We have analysed the hypervariable regions (HVR I and II) of human mitochondrial DNA (mtDNA) in individuals from Uttar Pradesh (UP), Bihar (BI) and Punjab (PUNJ), belonging to the Indo-European linguistic group, and from South India (SI), that have their linguistic roots in Dravidian language. Our analysis revealed the presence of known and novel mutations in both hypervariable regions in the studied population groups. Median joining network analyses based on mtDNA showed extensive overlap in mtDNA lineages despite the extensive cultural and linguistic diversity. MDS plot analysis based on Fst distances suggested increased maternal genetic proximity for the studied population groups compared with other world populations. Mismatch distribution curves, respective neighbour joining trees and other statistical analyses showed that there were significant expansions. The study revealed an ancient common ancestry for the studied population groups, most probably through common founder female lineage(s), and also indicated that human migrations occurred (maybe across and within the Indian subcontinent) even after the initial phase of female migration to India.
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Affiliation(s)
- Swarkar Sharma
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, 110067, New Delhi, India
| | - Anjana Saha
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, 110067, New Delhi, India
| | - Ekta Rai
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, 110067, New Delhi, India
| | - Audesh Bhat
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, 110067, New Delhi, India
| | - Ramesh Bamezai
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, 110067, New Delhi, India.
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190
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Pericić M, Lauc LB, Klarić IM, Rootsi S, Janićijevic B, Rudan I, Terzić R, Colak I, Kvesić A, Popović D, Sijacki A, Behluli I, Dordevic D, Efremovska L, Bajec DD, Stefanović BD, Villems R, Rudan P. High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations. Mol Biol Evol 2005; 22:1964-75. [PMID: 15944443 DOI: 10.1093/molbev/msi185] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The extent and nature of southeastern Europe (SEE) paternal genetic contribution to the European genetic landscape were explored based on a high-resolution Y chromosome analysis involving 681 males from seven populations in the region. Paternal lineages present in SEE were compared with previously published data from 81 western Eurasian populations and 5,017 Y chromosome samples. The finding that five major haplogroups (E3b1, I1b* (xM26), J2, R1a, and R1b) comprise more than 70% of SEE total genetic variation is consistent with the typical European Y chromosome gene pool. However, distribution of major Y chromosomal lineages and estimated expansion signals clarify the specific role of this region in structuring of European, and particularly Slavic, paternal genetic heritage. Contemporary Slavic paternal gene pool, mostly characterized by the predominance of R1a and I1b* (xM26) and scarcity of E3b1 lineages, is a result of two major prehistoric gene flows with opposite directions: the post-Last Glacial Maximum R1a expansion from east to west, the Younger Dryas-Holocene I1b* (xM26) diffusion out of SEE in addition to subsequent R1a and I1b* (xM26) putative gene flows between eastern Europe and SEE, and a rather weak extent of E3b1 diffusion toward regions nowadays occupied by Slavic-speaking populations.
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Affiliation(s)
- Marijana Pericić
- Institute for Anthropological Research, Amruseva 8, 10000 Zagreb, Croatia.
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191
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Flores C, Maca-Meyer N, Larruga JM, Cabrera VM, Karadsheh N, Gonzalez AM. Isolates in a corridor of migrations: a high-resolution analysis of Y-chromosome variation in Jordan. J Hum Genet 2005; 50:435-441. [PMID: 16142507 DOI: 10.1007/s10038-005-0274-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2005] [Accepted: 06/20/2005] [Indexed: 11/26/2022]
Abstract
A high-resolution, Y-chromosome analysis using 46 binary markers has been carried out in two Jordan populations, one from the metropolitan area of Amman and the other from the Dead Sea, an area geographically isolated. Comparisons with neighboring populations showed that whereas the sample from Amman did not significantly differ from their Levantine neighbors, the Dead Sea sample clearly behaved as a genetic outlier in the region. Its high R1*-M173 frequency (40%) has until now only been found in northern Cameroonian samples. This contrasts with the comparatively low presence of J representatives (9%), which is the modal clade in Middle Eastern populations, including Amman. The Dead Sea sample also showed a high presence of E3b3a-M34 lineages (31%), which is only comparable to that found in Ethiopians. Although ancient and recent ties with sub-Saharan and eastern Africans cannot be discarded, it seems that isolation, strong drift, and/or founder effects are responsible for the anomalous Y-chromosome pool of this population. These results demonstrate that, at a fine scale, the smooth, continental clines detected for several Y-chromosome markers are often disrupted by genetically divergent populations.
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Affiliation(s)
- Carlos Flores
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
- Unidad de Investigación, Hospital Universitario N.S. de Candelaria, 38010, Tenerife, Spain
| | - Nicole Maca-Meyer
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
- Unidad de Investigación, Hospital Universitario N.S. de Candelaria, 38010, Tenerife, Spain
| | - Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
| | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain
| | - Naif Karadsheh
- Department of Biochemistry and Physiology, Faculty of Medicine, University of Jordan, Amman, Jordan
| | - Ana M Gonzalez
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, 38271, Tenerife, Spain.
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192
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Movsessian AA. Phenetic Analysis in Paleoanthropology: Phenogeography of Peoples of the World. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0198-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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193
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The Indian Genome Variation database (IGVdb): a project overview. Hum Genet 2005; 118:1-11. [PMID: 16133172 DOI: 10.1007/s00439-005-0009-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2005] [Accepted: 05/26/2005] [Indexed: 12/15/2022]
Abstract
Indian population, comprising of more than a billion people, consists of 4693 communities with several thousands of endogamous groups, 325 functioning languages and 25 scripts. To address the questions related to ethnic diversity, migrations, founder populations, predisposition to complex disorders or pharmacogenomics, one needs to understand the diversity and relatedness at the genetic level in such a diverse population. In this backdrop, six constituent laboratories of the Council of Scientific and Industrial Research (CSIR), with funding from the Government of India, initiated a network program on predictive medicine using repeats and single nucleotide polymorphisms. The Indian Genome Variation (IGV) consortium aims to provide data on validated SNPs and repeats, both novel and reported, along with gene duplications, in over a thousand genes, in 15,000 individuals drawn from Indian subpopulations. These genes have been selected on the basis of their relevance as functional and positional candidates in many common diseases including genes relevant to pharmacogenomics. This is the first large-scale comprehensive study of the structure of the Indian population with wide-reaching implications. A comprehensive platform for Indian Genome Variation (IGV) data management, analysis and creation of IGVdb portal has also been developed. The samples are being collected following ethical guidelines of Indian Council of Medical Research (ICMR) and Department of Biotechnology (DBT), India. This paper reveals the structure of the IGV project highlighting its various aspects like genesis, objectives, strategies for selection of genes, identification of the Indian subpopulations, collection of samples and discovery and validation of genetic markers, data analysis and monitoring as well as the project's data release policy.
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194
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Wetton JH, Tsang KW, Khan H. Inferring the population of origin of DNA evidence within the UK by allele-specific hybridization of Y-SNPs. Forensic Sci Int 2005; 152:45-53. [PMID: 15878814 DOI: 10.1016/j.forsciint.2005.03.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 03/04/2005] [Indexed: 11/30/2022]
Abstract
Marked differences in Y-SNP allele frequencies between continental populations can be used to predict the biogeographic origin of a man's ancestral paternal lineage. Using 627 samples collected from individuals within the UK with pale-skinned Caucasian, dark-skinned Caucasian, African/Caribbean, South Asian, East Asian or Middle Eastern appearance we demonstrate that an individual's Y-SNP haplogroup is also strongly correlated with their physical appearance. Furthermore, experimental evaluation of the Marligen Signet Y-SNP kit in conjunction with the Luminex 100 detection instrument indicates that reliable and reproducible haplogrouping results can be obtained from 1 ng or more of target template derived from a variety of forensic evidence types including, blood, saliva and post-coital vaginal swabs. The test proved highly male-specific with reliable results being generated in the presence of a 1000-fold excess of female DNA, and no anomalous results were observed during degradation studies despite a gradual loss of typable loci. Hence, Y-SNP haplogrouping has considerable potential forensic utility in predicting likely ethnic appearance.
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Affiliation(s)
- Jon H Wetton
- The Forensic Science Service, R&D, Trident Court 2960, Solihull Parkway, Birmingham Business Park, Solihull B37 7YN, UK.
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195
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Majumder PP. Southward Ho! J Biosci 2005; 30:293-4. [PMID: 16052065 DOI: 10.1007/bf02703664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Partha P Majumder
- Human Genetics Unit, Indian Statistical Institute, 203, BT Road, Kolkata 700 108, India.
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196
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Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F, Taha A, Shaari NK, Raja JM, Ismail P, Zainuddin Z, Goodwin W, Bulbeck D, Bandelt HJ, Oppenheimer S, Torroni A, Richards M. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 2005; 308:1034-6. [PMID: 15890885 DOI: 10.1126/science.1109792] [Citation(s) in RCA: 557] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.
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Affiliation(s)
- Vincent Macaulay
- Department of Statistics, University of Glasgow, Glasgow G12 8QQ, Scotland, UK.
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197
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Thangaraj K, Chaubey G, Kivisild T, Reddy AG, Singh VK, Rasalkar AA, Singh L. Reconstructing the Origin of Andaman Islanders. Science 2005; 308:996. [PMID: 15890876 DOI: 10.1126/science.1109987] [Citation(s) in RCA: 173] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The origin of the Andaman "Negrito" and Nicobar "Mongoloid" populations has been ambiguous. Our analyses of complete mitochondrial DNA sequences from Onges and Great Andaman populations revealed two deeply branching clades that share their most recent common ancestor in founder haplogroup M, with lineages spread among India, Africa, East Asia, New Guinea, and Australia. This distribution suggests that these two clades have likely survived in genetic isolation since the initial settlement of the islands during an out-of-Africa migration by anatomically modern humans. In contrast, Nicobarese sequences illustrate a close genetic relationship with populations from Southeast Asia.
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198
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Achilli A, Rengo C, Battaglia V, Pala M, Olivieri A, Fornarino S, Magri C, Scozzari R, Babudri N, Santachiara-Benerecetti AS, Bandelt HJ, Semino O, Torroni A. Saami and Berbers--an unexpected mitochondrial DNA link. Am J Hum Genet 2005; 76:883-6. [PMID: 15791543 PMCID: PMC1199377 DOI: 10.1086/430073] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2005] [Accepted: 03/03/2005] [Indexed: 12/22/2022] Open
Abstract
The sequencing of entire human mitochondrial DNAs belonging to haplogroup U reveals that this clade arose shortly after the "out of Africa" exit and rapidly radiated into numerous regionally distinct subclades. Intriguingly, the Saami of Scandinavia and the Berbers of North Africa were found to share an extremely young branch, aged merely approximately 9,000 years. This unexpected finding not only confirms that the Franco-Cantabrian refuge area of southwestern Europe was the source of late-glacial expansions of hunter-gatherers that repopulated northern Europe after the Last Glacial Maximum but also reveals a direct maternal link between those European hunter-gatherer populations and the Berbers.
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Affiliation(s)
- Alessandro Achilli
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Chiara Rengo
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Vincenza Battaglia
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Maria Pala
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Anna Olivieri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Simona Fornarino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Chiara Magri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Rosaria Scozzari
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Nora Babudri
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - A. Silvana Santachiara-Benerecetti
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Hans-Jürgen Bandelt
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Ornella Semino
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
| | - Antonio Torroni
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy; Dipartimento di Genetica e Biologia Molecolare, Università “La Sapienza,” Rome; Dipartimento di Biologia Cellulare e Ambientale, Università di Perugia, Perugia, Italy; and Fachbereich Mathematik, Universität Hamburg, Hamburg
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199
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Rajkumar R, Banerjee J, Gunturi HB, Trivedi R, Kashyap VK. Phylogeny and antiquity of M macrohaplogroup inferred from complete mt DNA sequence of Indian specific lineages. BMC Evol Biol 2005; 5:26. [PMID: 15804362 PMCID: PMC1079809 DOI: 10.1186/1471-2148-5-26] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Accepted: 04/02/2005] [Indexed: 12/04/2022] Open
Abstract
Background Analysis of human complete mitochondrial DNA sequences has largely contributed to resolve phylogenies and antiquity of different lineages belonging to the majorhaplogroups L, N and M (East-Asian lineages). In the absence of whole mtDNA sequence information of M lineages reported in India that exhibits highest diversity within the sub-continent, the present study was undertaken to provide a detailed analysis of this macrohaplogroup to precisely characterize and unravel the intricate phylogeny of the lineages and to establish the antiquity of M lineages in India. Results The phylogenetic tree constructed from sequencing information of twenty-four whole mtDNA genome revealed novel substitutions in the previously defined M2a and M6 lineages. The most striking feature of this phylogenetic tree is the recognition of two new lineages, M30 and M31, distinguished by transitions at 12007 and 5319, respectively. M30 comprises of M18 and identifies a potential new sub-lineage possessing substitution at 16223 and 16300. It further branches into M30a sub-lineage, defined by 15431 and 195A substitution. The age of M30 lineage was estimated at 33,042 YBP, indicating a more recent expansion time than M2 (49,686 YBP). The M31 branch encompasses the M6 lineage along with the previously defined M3 and M4 lineages. Contradictory to earlier reports, the M5 lineage does not always include a 12477 substitution, and is more appropriately defined by a transversion at 10986A. The phylogenetic tree also identifies a potential new lineage in the M* branch with HVSI sequence as 16223,16325. Substitutions in M25 were in concordance with previous reports. Conclusion This study describes five new basal mutations and recognizes two new lineages, M30 and M31 that substantially contribute to the present understanding of macrohaplogroup M. These two newly erected lineages include the previously independent lineages M18 and M6 as sub-lineages within them, respectively, suggesting that most mt DNA genomes might arise as limited offshoots of M trunk. Furthermore, this study supports the non existence of lineages such as M3 and M4 that are solely defined on the basis of fast mutating control region motifs and hence, establishes the importance of coding region markers for an accurate understanding of the phylogeny. The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.
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Affiliation(s)
- Revathi Rajkumar
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata- 70014, India
| | - Jheelam Banerjee
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata- 70014, India
| | - Hima Bindu Gunturi
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata- 70014, India
| | - R Trivedi
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata- 70014, India
| | - VK Kashyap
- National DNA Analysis Centre, Central Forensic Science Laboratory, 30 Gorachand Road, Kolkata- 70014, India
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200
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Thangaraj K, Sridhar V, Kivisild T, Reddy AG, Chaubey G, Singh VK, Kaur S, Agarawal P, Rai A, Gupta J, Mallick CB, Kumar N, Velavan TP, Suganthan R, Udaykumar D, Kumar R, Mishra R, Khan A, Annapurna C, Singh L. Different population histories of the Mundari- and Mon-Khmer-speaking Austro-Asiatic tribes inferred from the mtDNA 9-bp deletion/insertion polymorphism in Indian populations. Hum Genet 2005; 116:507-17. [PMID: 15772853 DOI: 10.1007/s00439-005-1271-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 01/13/2005] [Indexed: 12/01/2022]
Abstract
Length variation in the human mtDNA intergenic region between the cytochrome oxidase II (COII) and tRNA lysine (tRNA(lys)) genes has been widely studied in world populations. Specifically, Austronesian populations of the Pacific and Austro-Asiatic populations of southeast Asia most frequently carry the 9-bp deletion in that region implying their shared common ancestry in haplogroup B. Furthermore, multiple independent origins of the 9-bp deletion at the background of other mtDNA haplogroups has been shown in populations of Africa, Europe, Australia, and India. We have analyzed 3293 Indian individuals belonging to 58 populations, representing different caste, tribal, and religious groups, for the length variation in the 9-bp motif. The 9-bp deletion (one copy) and insertion (three copies) alleles were observed in 2.51% (2.15% deletion and 0.36% insertion) of the individuals. The maximum frequency of the deletion (45.8%) was observed in the Nicobarese in association with the haplogroup B5a D-loop motif that is common throughout southeast Asia. The low polymorphism in the D-loop sequence of the Nicobarese B5a samples suggests their recent origin and a founder effect, probably involving migration from southeast Asia. Interestingly, none of the 302 (except one Munda sample, which has 9-bp insertion) from Mundari-speaking Austro-Asiatic populations from the Indian mainland showed the length polymorphism of the 9-bp motif, pointing either to their independent origin from the Mon-Khmeric-speaking Nicobarese or to an extensive admixture with neighboring Indo-European-speaking populations. Consistent with previous reports, the Indo-European and Dravidic populations of India showed low frequency of the 9-bp deletion/insertion. More than 18 independent origins of the deletion or insertion mutation could be inferred in the phylogenetic analysis of the D-loop sequences.
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Affiliation(s)
- Kumarasamy Thangaraj
- Centre for Cellular and Molecular biology, Uppal Road, Hyderabad, 500 007, India
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